Retrieve quantitation types of a dataset

get_dataset_quantitation_types(
  dataset,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

dataset: A numerical dataset identifier or a dataset short name
raw: TRUE to receive results as-is from Gemma, or FALSE to enable parsing. Raw results usually contain additional fields and flags that are omitted in the parsed results.
memoised: Whether or not to save to cache for future calls with the same inputs and use the result saved in cache if a result is already saved. Doing options(gemma.memoised = TRUE) will ensure that the cache is always used. Use forget_gemma_memoised to clear the cache.
file: The name of a file to save the results to, or NULL to not write results to a file. If raw == TRUE, the output will be the raw endpoint from the API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.
overwrite: Whether or not to overwrite if a file exists at the specified filename.

Value

A data.table containing the quantitation types

The fields of the output data.table are:

id: If of the quantitation type. Any raw quantitation type can be accessed by get_dataset_raw_expression function using this id.
name: Name of the quantitation type
description: Description of the quantitation type
type: Type of the quantitation type. Either raw or processed. Each dataset will have one processed quantitation type which is the data returned using get_dataset_processed_expression
ratio: Whether or not the quanitation type is a ratio of multiple quantitation types. Typically TRUE for processed TWOCOLOR quantitation type.
preferred: The preferred raw quantitation type. This version is used in generation of the processed data within gemma.
recomputed: If TRUE this quantitation type is generated by recomputing raw data files Gemma had access to.

Examples

get_dataset_quantitation_types("GSE59918")
#>        id                        name
#>     <int>                      <char>
#> 1: 535697                        RPKM
#> 2: 535696                      Counts
#> 3: 535695 log2cpm - Processed version
#> 4: 535694                     log2cpm
#>                                                                                      description
#>                                                                                           <char>
#> 1:                                   Reads (or fragments) per kb of gene model per million reads
#> 2:                                                                    Read counts for gene model
#> 3: Processed data (as per Gemma) for analysis, based on the preferred quantitation type raw data
#> 4:                                                     log-2 transformed read counts per million
#>         type  ratio  scale preferred recomputed
#>       <char> <lgcl> <char>    <lgcl>     <lgcl>
#> 1:       raw  FALSE LINEAR     FALSE       TRUE
#> 2:       raw  FALSE  COUNT     FALSE       TRUE
#> 3: processed  FALSE   LOG2     FALSE       TRUE
#> 4:       raw  FALSE   LOG2      TRUE       TRUE